Particle system emitting upside down
Ok I took a look at your file, You had to fix the rotation of two things. 


Change the rotation for the particles to Global Z
Go back to your other layer and rotate the group as shown in the image
You had the pivot point at the top of all your buildings, So Blender assumes this is where the building should start. You need to select each building in edit mode, then select the bottom face, hit Shift + S and choose move cursor to selected. Hit tab to go back to object mode and on the left tool bar change pivot point to 3D cursor. 


You need to do this to every building in the group.

 



Or you can just use the fixed blend file.